Copy Number Segments Plot

Generates a plot of all CN segments for a specified region.

focal_cn_plot(
  region,
  gene,
  these_samples_metadata,
  this_seq_type = "genome",
  type = "gain",
  segment_size = 1,
  crop_segments = TRUE,
  sort_by_annotation = c("pathology"),
  crop_distance = 1e+08
)

Arguments

region

Genomic region for plotting in bed format.

gene

Optional variable, converts gene to region if region not supplied.

these_samples_metadata

Required parameter. GAMBL metadata subset to the cases you want to process (or full metadata).

this_seq_type

Seq type for returned CN segments. One of "genome" (default) or "capture".

type

Type of CN segment to be plotted. Default is gain (CN > 2).

segment_size

This parameter controls the size of the segment plotted with ggplot2, default is 1.

crop_segments

Boolean statement that crops segment by first checking if crop segment is smaller than lef/right distance, then adds or subtracts crop distance to end/start coordinates. Default is TRUE.

sort_by_annotation

Sort CN by annotation, default is "pathology".

crop_distance

Crop distance for cropping segments. Default value is 10000000 bp.

Value

Nothing

Details

This function visualizes all CN segments for a defined region, colours the returned segments based on lymphgen information. In addition, this function takes either a specified region (chr:start-end format). If no region is supplied, the user can give the function a gene symbol with gene. If so, the function will internally retrieve the region for the specified gene. Sample IDs are specified along the y-axis and the genomic position is visualized along the x-axis.

Examples

#get metadata
this_metadata = get_gambl_metadata()

#get myc region
myc_region = gene_to_region(gene_symbol = "MYC",
                            return_as = "region")
#> 1 region(s) returned for 1 gene(s)

#build plot
focal_cn_plot(these_samples_metadata = this_metadata,
              region = myc_region,
              type = "loss",
              crop_distance = 100000000)